@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/esm/LinearSNPCoverageDisplay/components/Tooltip.js.map

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package/esm/LinearSNPCoverageDisplay/index.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function register(pluginManager: PluginManager): void;

package/esm/LinearSNPCoverageDisplay/index.js

@@ -0,0 +1,18 @@
+import configSchemaFactory from './models/configSchema';
+import modelFactory from './models/model';
+import { LinearWiggleDisplayReactComponent } from '@jbrowse/plugin-wiggle';
+import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
+export default function register(pluginManager) {
+    pluginManager.addDisplayType(() => {
+        const configSchema = configSchemaFactory(pluginManager);
+        return new DisplayType({
+            name: 'LinearSNPCoverageDisplay',
+            configSchema,
+            stateModel: modelFactory(pluginManager, configSchema),
+            trackType: 'AlignmentsTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: LinearWiggleDisplayReactComponent,
+        });
+    });
+}
+//# sourceMappingURL=index.js.map

package/esm/LinearSNPCoverageDisplay/index.js.map

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package/esm/LinearSNPCoverageDisplay/models/configSchema.d.ts

@@ -0,0 +1,2 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function SNPCoverageConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration").AnyConfigurationSchemaType;

package/esm/LinearSNPCoverageDisplay/models/configSchema.js

@@ -0,0 +1,44 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view';
+import { types } from 'mobx-state-tree';
+export default function SNPCoverageConfigFactory(pluginManager) {
+    const SNPCoverageRendererConfigSchema = pluginManager.getRendererType('SNPCoverageRenderer').configSchema;
+    return ConfigurationSchema('LinearSNPCoverageDisplay', {
+        autoscale: {
+            type: 'stringEnum',
+            defaultValue: 'local',
+            model: types.enumeration('Autoscale type', ['local']),
+            description: 'performs local autoscaling (no other options for SNP Coverage available)',
+        },
+        minScore: {
+            type: 'number',
+            defaultValue: Number.MIN_VALUE,
+            description: 'minimum value for the y-scale',
+        },
+        maxScore: {
+            type: 'number',
+            description: 'maximum value for the y-scale',
+            defaultValue: Number.MAX_VALUE,
+        },
+        scaleType: {
+            type: 'stringEnum',
+            model: types.enumeration('Scale type', ['linear', 'log']),
+            description: 'The type of scale to use',
+            defaultValue: 'linear',
+        },
+        inverted: {
+            type: 'boolean',
+            description: 'draw upside down',
+            defaultValue: false,
+        },
+        multiTicks: {
+            type: 'boolean',
+            description: 'Display multiple values for the ticks',
+            defaultValue: false,
+        },
+        renderers: ConfigurationSchema('RenderersConfiguration', {
+            SNPCoverageRenderer: SNPCoverageRendererConfigSchema,
+        }),
+    }, { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true });
+}
+//# sourceMappingURL=configSchema.js.map

package/esm/LinearSNPCoverageDisplay/models/configSchema.js.map

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package/esm/LinearSNPCoverageDisplay/models/model.d.ts

@@ -0,0 +1,348 @@
+/// <reference types="react" />
+import { AnyConfigurationSchemaType, AnyConfigurationModel } from '@jbrowse/core/configuration';
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const stateModelFactory: (pluginManager: PluginManager, configSchema: AnyConfigurationSchemaType) => import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+} & {
+    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+        key: import("mobx-state-tree").ISimpleType<string>;
+        region: import("mobx-state-tree").IModelType<{
+            refName: import("mobx-state-tree").ISimpleType<string>;
+            start: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    }, {
+        renderInProgress: AbortController | undefined;
+        filled: boolean;
+        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+        layout: any;
+        status: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: any;
+        }) => any;
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(abortController: AbortController): void;
+        setMessage(messageText: string): void;
+        setRendered(props: {
+            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            features: Map<string, import("@jbrowse/core/util").Feature>;
+            layout: any;
+            maxHeightReached: boolean;
+            renderProps: any;
+        } | undefined): void;
+        setError(error: unknown): void;
+        reload(): void;
+        beforeDestroy(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
+    configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
+    selectedRendering: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    resolution: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    fill: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    color: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    posColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    negColor: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    summaryScoreMode: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    rendererTypeNameState: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    scale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    autoscale: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    displayCrossHatches: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    constraints: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
+        max: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+        min: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"LinearSNPCoverageDisplay">;
+    drawInterbaseCounts: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    drawIndicators: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    drawArcs: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
+        flagInclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+        flagExclude: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+        readName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        tagFilter: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+            tag: import("mobx-state-tree").ISimpleType<string>;
+            value: import("mobx-state-tree").ISimpleType<string>;
+        }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
+        type: import("mobx-state-tree").ISimpleType<string>;
+        tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+}, {
+    rendererTypeName: string;
+    error: unknown;
+} & {
+    readonly RenderingComponent: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        onHorizontalScroll?: Function | undefined;
+        blockState?: Record<string, any> | undefined;
+    }>;
+    readonly DisplayBlurb: import("react").FC<{
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            rendererTypeName: string;
+            error: unknown;
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            type: import("mobx-state-tree").ISimpleType<string>;
+            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+        }, {
+            rendererTypeName: string;
+            error: unknown;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    }> | null;
+    readonly adapterConfig: any;
+    readonly parentTrack: any;
+    renderProps(): any;
+    readonly rendererType: any;
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
+    regionCannotBeRendered(): undefined;
+} & {
+    setError(error?: unknown): void;
+    setRpcDriverName(rpcDriverName: string): void;
+    reload(): void;
+} & {
+    currBpPerPx: number;
+    message: string;
+    featureIdUnderMouse: string | undefined;
+    contextMenuFeature: import("@jbrowse/core/util").Feature | undefined;
+    scrollTop: number;
+    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
+    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
+} & {
+    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
+} & {
+    readonly renderDelay: number;
+    readonly TooltipComponent: import("react").FC<any>;
+    readonly selectedFeatureId: string | undefined;
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
+} & {
+    readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
+    readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    getFeatureOverlapping(blockKey: string, x: number, y: number): any;
+    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
+    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    readonly currentBytesRequested: number;
+    readonly currentFeatureScreenDensity: number;
+    readonly maxFeatureScreenDensity: any;
+    readonly estimatedStatsReady: boolean;
+    readonly maxAllowableBytes: number;
+} & {
+    setMessage(message: string): void;
+    afterAttach(): void;
+    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
+        headers?: Record<string, string> | undefined;
+        signal?: AbortSignal | undefined;
+        filters?: string[] | undefined;
+    }): Promise<{}>;
+    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
+    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
+    clearRegionStats(): void;
+    setHeight(displayHeight: number): number;
+    resizeHeight(distance: number): number;
+    setScrollTop(scrollTop: number): void;
+    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
+    addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
+    setCurrBpPerPx(n: number): void;
+    deleteBlock(key: string): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    clearFeatureSelection(): void;
+    setFeatureIdUnderMouse(feature: string | undefined): void;
+    reload(): void;
+    setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
+} & {
+    readonly regionTooLarge: boolean;
+    readonly regionTooLargeReason: string;
+} & {
+    reload(): Promise<void>;
+    afterAttach(): void;
+} & {
+    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
+    trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    contextMenuItems(): {
+        label: string;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
+        onClick: () => void;
+    }[];
+    renderProps(): any;
+} & {
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
+        overrideHeight: number;
+    }): Promise<JSX.Element>;
+} & {
+    statsReady: boolean;
+    message: string | undefined;
+    stats: {
+        scoreMin: number;
+        scoreMax: number;
+    };
+    statsFetchInProgress: AbortController | undefined;
+} & {
+    updateStats({ scoreMin, scoreMax, }: {
+        scoreMin: number;
+        scoreMax: number;
+    }): void;
+    setColor(color: string): void;
+    setPosColor(color: string): void;
+    setNegColor(color: string): void;
+    setLoading(aborter: AbortController): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    setResolution(res: number): void;
+    setFill(fill: boolean): void;
+    toggleLogScale(): void;
+    setScaleType(scale?: string | undefined): void;
+    setSummaryScoreMode(val: string): void;
+    setAutoscale(val: string): void;
+    setMaxScore(val?: number | undefined): void;
+    setRendererType(val: string): void;
+    setMinScore(val?: number | undefined): void;
+    toggleCrossHatches(): void;
+    setCrossHatches(cross: boolean): void;
+} & {
+    readonly TooltipComponent: import("react").FC<{}>;
+    readonly adapterTypeName: any;
+    readonly rendererTypeName: string;
+    readonly filters: undefined;
+    readonly scaleType: any;
+    readonly maxScore: any;
+    readonly minScore: any;
+} & {
+    readonly rendererConfig: any;
+} & {
+    readonly filled: any;
+    readonly summaryScoreModeSetting: any;
+    readonly domain: number[];
+    readonly needsScalebar: boolean;
+    readonly scaleOpts: {
+        domain: number[];
+        stats: {
+            scoreMin: number;
+            scoreMax: number;
+        };
+        autoscaleType: any;
+        scaleType: any;
+        inverted: any;
+    };
+    readonly canHaveFill: boolean;
+    readonly autoscaleType: any;
+    readonly displayCrossHatchesSetting: any;
+} & {
+    readonly ticks: any;
+} & {
+    renderProps(): any;
+    readonly adapterCapabilities: string[];
+    readonly hasResolution: boolean;
+    readonly hasGlobalStats: boolean;
+} & {
+    trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+        type: string;
+        label: string;
+        checked: any;
+        onClick: () => void;
+    })[];
+} & {
+    reload(): Promise<void>;
+    afterAttach(): void;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
+        overrideHeight: number;
+    }): Promise<JSX.Element>;
+} & {
+    modificationTagMap: import("mobx").ObservableMap<any, any>;
+} & {
+    setConfig(configuration: AnyConfigurationModel): void;
+    setFilterBy(filter: {
+        flagInclude: number;
+        flagExclude: number;
+        readName?: string;
+        tagFilter?: {
+            tag: string;
+            value: string;
+        };
+    }): void;
+    setColorBy(colorBy?: {
+        type: string;
+        tag?: string;
+    }): void;
+    updateModificationColorMap(uniqueModifications: string[]): void;
+} & {
+    readonly rendererConfig: any;
+    readonly drawArcsSetting: any;
+    readonly drawInterbaseCountsSetting: any;
+    readonly drawIndicatorsSetting: any;
+    readonly modificationsReady: boolean;
+    renderProps(): any;
+} & {
+    toggleDrawIndicators(): void;
+    toggleDrawInterbaseCounts(): void;
+    toggleDrawArcs(): void;
+    afterAttach(): void;
+} & {
+    readonly TooltipComponent: (props: {
+        model: any;
+        height: number;
+        offsetMouseCoord: [number, number];
+        clientMouseCoord: [number, number];
+        clientRect?: DOMRect | undefined;
+    }) => JSX.Element | null;
+    readonly adapterConfig: {
+        type: string;
+        subadapter: any;
+    };
+    readonly rendererTypeName: string | undefined;
+    readonly needsScalebar: boolean;
+    contextMenuItems(): never[];
+    trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+        label: string;
+        type: string;
+        checked: any;
+        onClick: () => void;
+    })[];
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export declare type SNPCoverageDisplayModel = ReturnType<typeof stateModelFactory>;
+export default stateModelFactory;

package/esm/LinearSNPCoverageDisplay/models/model.js

@@ -0,0 +1,185 @@
+import { addDisposer, types, cast, getEnv, getSnapshot } from 'mobx-state-tree';
+import { observable, autorun } from 'mobx';
+import { getConf, readConfObject, } from '@jbrowse/core/configuration';
+import { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle';
+import { getContainingView } from '@jbrowse/core/util';
+import Tooltip from '../components/Tooltip';
+import { getUniqueModificationValues } from '../../shared';
+// using a map because it preserves order
+const rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
+const stateModelFactory = (pluginManager, configSchema) => types
+    .compose('LinearSNPCoverageDisplay', linearWiggleDisplayModelFactory(pluginManager, configSchema), types.model({
+    type: types.literal('LinearSNPCoverageDisplay'),
+    drawInterbaseCounts: types.maybe(types.boolean),
+    drawIndicators: types.maybe(types.boolean),
+    drawArcs: types.maybe(types.boolean),
+    filterBy: types.optional(types.model({
+        flagInclude: types.optional(types.number, 0),
+        flagExclude: types.optional(types.number, 1540),
+        readName: types.maybe(types.string),
+        tagFilter: types.maybe(types.model({ tag: types.string, value: types.string })),
+    }), {}),
+    colorBy: types.maybe(types.model({
+        type: types.string,
+        tag: types.maybe(types.string),
+    })),
+}))
+    .volatile(() => ({
+    modificationTagMap: observable.map({}),
+}))
+    .actions(self => ({
+    setConfig(configuration) {
+        self.configuration = configuration;
+    },
+    setFilterBy(filter) {
+        self.filterBy = cast(filter);
+    },
+    setColorBy(colorBy) {
+        self.colorBy = cast(colorBy);
+    },
+    updateModificationColorMap(uniqueModifications) {
+        const colorPalette = ['red', 'blue', 'green', 'orange', 'purple'];
+        let i = 0;
+        uniqueModifications.forEach(value => {
+            if (!self.modificationTagMap.has(value)) {
+                const newColor = colorPalette[i++];
+                self.modificationTagMap.set(value, newColor);
+            }
+        });
+    },
+}))
+    .views(self => {
+    const { renderProps: superRenderProps } = self;
+    return {
+        get rendererConfig() {
+            var _a, _b, _c;
+            const configBlob = getConf(self, ['renderers', self.rendererTypeName]) || {};
+            return self.rendererType.configSchema.create({
+                ...configBlob,
+                drawInterbaseCounts: (_a = self.drawInterbaseCounts) !== null && _a !== void 0 ? _a : configBlob.drawInterbaseCounts,
+                drawIndicators: (_b = self.drawIndicators) !== null && _b !== void 0 ? _b : configBlob.drawIndicators,
+                drawArcs: (_c = self.drawArcs) !== null && _c !== void 0 ? _c : configBlob.drawArcs,
+            }, getEnv(self));
+        },
+        get drawArcsSetting() {
+            var _a;
+            return ((_a = self.drawArcs) !== null && _a !== void 0 ? _a : readConfObject(this.rendererConfig, 'drawArcs'));
+        },
+        get drawInterbaseCountsSetting() {
+            var _a;
+            return ((_a = self.drawInterbaseCounts) !== null && _a !== void 0 ? _a : readConfObject(this.rendererConfig, 'drawInterbaseCounts'));
+        },
+        get drawIndicatorsSetting() {
+            var _a;
+            return ((_a = self.drawIndicators) !== null && _a !== void 0 ? _a : readConfObject(this.rendererConfig, 'drawIndicators'));
+        },
+        get modificationsReady() {
+            var _a;
+            return ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) === 'modifications'
+                ? Object.keys(JSON.parse(JSON.stringify(self.modificationTagMap)))
+                    .length > 0
+                : true;
+        },
+        renderProps() {
+            const superProps = superRenderProps();
+            const { colorBy, filterBy, modificationTagMap } = self;
+            return {
+                ...superProps,
+                notReady: superProps.notReady || !this.modificationsReady,
+                modificationTagMap: Object.fromEntries(modificationTagMap.toJSON()),
+                // must use getSnapshot because otherwise changes to e.g. just the
+                // colorBy.type are not read
+                colorBy: colorBy ? getSnapshot(colorBy) : undefined,
+                filterBy: filterBy ? getSnapshot(filterBy) : undefined,
+            };
+        },
+    };
+})
+    .actions(self => ({
+    toggleDrawIndicators() {
+        self.drawIndicators = !self.drawIndicatorsSetting;
+    },
+    toggleDrawInterbaseCounts() {
+        self.drawInterbaseCounts = !self.drawInterbaseCountsSetting;
+    },
+    toggleDrawArcs() {
+        self.drawArcs = !self.drawArcsSetting;
+    },
+    afterAttach() {
+        addDisposer(self, autorun(async () => {
+            try {
+                const { colorBy } = self;
+                const { staticBlocks } = getContainingView(self);
+                if (!self.estimatedStatsReady) {
+                    return;
+                }
+                if (self.regionTooLarge) {
+                    return;
+                }
+                if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
+                    const vals = await getUniqueModificationValues(self, getConf(self.parentTrack, 'adapter'), colorBy, staticBlocks);
+                    self.updateModificationColorMap(vals);
+                }
+            }
+            catch (error) {
+                console.error(error);
+                self.setError(error);
+            }
+        }, { delay: 1000 }));
+    },
+}))
+    .views(self => {
+    const { trackMenuItems: superTrackMenuItems } = self;
+    return {
+        get TooltipComponent() {
+            return Tooltip;
+        },
+        get adapterConfig() {
+            const subadapter = getConf(self.parentTrack, 'adapter');
+            return {
+                type: 'SNPCoverageAdapter',
+                subadapter,
+            };
+        },
+        get rendererTypeName() {
+            return rendererTypes.get('snpcoverage');
+        },
+        get needsScalebar() {
+            return true;
+        },
+        contextMenuItems() {
+            return [];
+        },
+        trackMenuItems() {
+            return [
+                ...superTrackMenuItems(),
+                {
+                    label: 'Draw insertion/clipping indicators',
+                    type: 'checkbox',
+                    checked: self.drawIndicatorsSetting,
+                    onClick: () => {
+                        self.toggleDrawIndicators();
+                    },
+                },
+                {
+                    label: 'Draw insertion/clipping counts',
+                    type: 'checkbox',
+                    checked: self.drawInterbaseCountsSetting,
+                    onClick: () => {
+                        self.toggleDrawInterbaseCounts();
+                    },
+                },
+                {
+                    label: 'Draw arcs',
+                    type: 'checkbox',
+                    checked: self.drawArcsSetting,
+                    onClick: () => {
+                        self.toggleDrawArcs();
+                    },
+                },
+            ];
+        },
+    };
+});
+export default stateModelFactory;
+//# sourceMappingURL=model.js.map

package/esm/LinearSNPCoverageDisplay/models/model.js.map

@@ -0,0 +1 @@
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package/esm/NestedFrequencyTable.d.ts

@@ -0,0 +1,14 @@
+export default class NestedFrequencyTable {
+    categories: {
+        [key: string]: any;
+    };
+    constructor(initialData?: {});
+    total(): number;
+    decrement(slotName: string, amount: number): any;
+    increment(slotName: string, amount: number): any;
+    get(slotName: string): any;
+    getNested(path: string | string[]): any;
+    toString(): string;
+    valueOf(): number;
+    forEach(func: Function, ctx: any): void;
+}